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Standard Tools

These are the tools we have pretty much settled on as a team.  For ease and consistency of development please try to remain on these tools and discuss with the team before introducing competing technologies.

  • Operating System: what ever floats your boat.
  • IDE: Eclipse commonly used and free
  • Wiki / Issue Tracker / Code Browsing and Reviewing / Automated Builds: we have a Jira Studio subscription  (Nicole Deflaux and Mike Kellen as admins)
  • Code versioning: Subversion, hosted by Atlassian as part of our Jira Studio subscription
  • Build System: Maven
  • Build repository manager: see Sage's hosted Artifactory service see jFrog website for info (John Hill and Mike Kellen as admins)

Profilers

Code Coverage

We have been approved for free licenses to use Clover (Atlassian Code Coverage tool) for Eclipse. To install the Clover plug-in for eclipse you can use the update site http://update.atlassian.com/eclipse/clover

Eclipse users: Within Eclipse, select from the menu "Window > Preferences" and click on "Clover > License" and paste the above license string into the license text area.

MONqrDkXrjMnJciwRtLBAEGFOmnBGjNmbRRWECCaUafBQo
mi2Kehqg3mIlkHdhHlTejumx2KzaGJQIsBkyJf66uTXT7W
NPQQsvpRQnqmPnrRpQPSunQNrOQnnRqMNovXXwssmXtvsW
vSttxsuurRqopnmomUUnovrnuoummmmmUUnovrnuoummmm
mUUJXdbW2flkbqtlohpUUnmmmm

Java

Libraries

At this point we don't have any strict licensing requirements, however to maintain flexibility we have to be careful about licenses for software we choose to incorporate into our system.  The best licenses are open source licenses without copy-left provisions (e.g. Apache License) that give us maximal flexibility in what we later do with the code base.  Some strong copy-left licenses (e.g. GPL) would impose licensing requirements on us (e.g. force us to use GPL ourselves) if we chose to redistribute the code base at a later date. For now, we should just be aware of the mix of licenses incorporated into our projects, and have a bias for open source, non-copy left licenses.

  • Application Framework: Spring
  • Test: JUnit as test framework, Easy Mock 3.0 for mock objects in unit tests 
  • Mock Objects: Use Mockito to Mock up objects for tests.

R

Python

Python Examples for Perl programmers

  1. Example: empty dictionary, add values to it 
    layer = {}
layer["type"] = row[1]
layer["status"] = row[2]
layer["name"] = row[3]
layer["numSamples"] = row[4]
layer["platform"] = row[5]
layer["version"] = row[6]
layer["qcBy"] = row[11]
  2. Example: empty two level dictionary, add values to it 
    layer = {}
layer['foo'] = {}
layer['foo']['bar'] = 3
layer['hello'] = {}
layer['hello']['world'] = 42
  3. Example: create a populated dictionary 
    CSV_TO_PRIMARY_FIELDS = {
    'name': 'name',
    'description': 'description',
    'Investigator': 'creator',
    'Creation Date': 'creationDate',
    'Status': 'status',
    'date_released': 'releaseDate',
    'version':'version'
    }
  4. Example: create a populated two-level dictionary 
    MY_FAKE_LAYER = {'foo': {'bar': 3}, 'hello': {'world': 42}}
  5. Example: empty array, add values to it 
    stringAnnotations = []
    stringAnnotations.append("foo")
  6. Example: create a populated array 
    CSV_SKIP_FIELDS = ["db_id","user_agreement_file_path", "readme_file_path"];

MySQL

Subversion

For general SVN info see the SVN book

Moving files and directories

The eclipse plugin for svn generally does a decent job moving files and directories. See also http://svnbook.red-bean.com/en/1.1/re18.html

Here is an example:

svn gets really upset though when you do more complicated things like created a file, delete that file, then make a directory with the same name in the same location as the deleted file. (but that is a pretty odd thing to do anyway)

When in doubt, make a developer branch and try it there first.http://svnbook.red-bean.com/en/1.1/ch04s02.html#svn-ch-4-sect-2.1

Developer branches

Want to make a drastic change and run it by the team before merging it to trunk? Want to check in broken code? Make a branch and do it there.

Resources

How to Set Up Merge Tracking

  1. Download svnmerge.py
  2. Make a branch directory for yourself (you'll only need to do this once) 
    svn mkdir https://sagebionetworks.jira.com/svn/PLFM/branches/deflaux
  3. Make a new branch from trunk 
    svn copy https://sagebionetworks.jira.com/svn/PLFM/trunk https://sagebionetworks.jira.com/svn/PLFM/branches/deflaux/automatedIntegrationTesting
  4. Have both trunk and your new branch on your local hard drive, this assumes you already have trunk checked out in directory ~/platform 
    cd ~/platform
svn update trunk
svn checkout https://sagebionetworks.jira.com/svn/PLFM/branches/deflaux/automatedIntegrationTesting
  5. Initialize merge tracking 
    cd trunk
svnmerge.py init ../automatedIntegrationTesting
svn commit -F svnmerge-commit-message.txt
cd ../automatedIntegrationTesting
svnmerge.py init ../trunk
svn commit -F svnmerge-commit-message.txt

How to merge

Merge from trunk to your branch

Best Practice: merge changes from trunk to your branch every morning Monday through Friday. This reduces the pain later when you want to merge from your branch to trunk.

  1. Ensure the branch is working and committed to SVN.
  2. To see what changes and/or branches are available for importing, use this command from the branch distribution: 
    python svnmerge.py avail -l
    • Windows Users: One of the results should be '/PLFM/trunk'.
  3. import the changes from trunk into the branch:
    • to merge all changes 
      python svnmerge.py merge
    • to merge one or more particular changes 
      python svnmerge.py merge -r #,#,#
    • Windows Users: to merge all changes 
      python svnmerge.py merge -S /PLFM/trunk
  4. Resolve conflicts, compile, test and commit EVERYTHING in the branch. 
    svn ci -F svnmerge-commit-message.txt

Merge from your branch to trunk

  1. Go to an up-to-date local distribution of trunk.
  2. From the trunk distribution use the 'avail' command (above) to find the branch of interest.
  3. Use the following command to find the revision(s) of interest: 
    python svnmerge.py avail -S <your branch>
  4. Import the changes from the branch into trunk:
    1. For all changes 
      python svnmerge.py merge -S <your branch>
    2. For particular changes 
      python svnmerge.py merge -r <your revisions comma separated> -S <your branch>
  5. Resolve conflicts, compile, test and commit.

Elastic Bamboo

We currently have MySQL running on our Elastic Bamboo host for the purposes of integration testing. This is accomplished by the customise-extras.sh shell script which is run at boot time for the hosts.

If you want to import a database dump, install Crowd, etc., here is how to modify that script:

  1. Log onto the currently running elastic instance (or spawn one if none are running). http://confluence.atlassian.com/display/BAMBOO/Accessing+an+Elastic+Instance
    • Note that the ssh key is on belltown:/work/platform/PasswordsAndCredentials/AtlassianAccountAWSCredentials/elasticbamboo.pk
    • Note that if you want to log onto the AWS console, Mike's username and password is on belltown:/work/platform/PasswordsAndCredentials/AtlassianAccountAWSCredentials/Mike'sPassword
  2. From the shell try out the commands you want to run at boot time
  3. Run you build and make sure it works
  4. Check your changes to customize-extras.sh into source control PLFM/trunk/tools/bamboo/bin/customise-extras.sh
  5. On the bamboo host, overwrite /mnt/bamboo-ebs/bin/customise-extras.sh with your updated script.
  6. Follow these instructions to create snapshot and configure bamboo to use it Updating your EBS snapshot
  7. Shutdown the host, and kick off a new build. This should start a new bamboo host that will run your updated script.
  8. Make sure the build passes!

For more information, see:

Tools To Know About

Pretty-Print JSON

Have a large blob of JSON?  Want to see it in human readable format?  Toss it into this web ui: http://jsonformatter.curiousconcept.com/

Web Trace Tools

UML Tools

Class Diagrams

UMLet 11.2 is a "Free UML Tool for Fast UML Diagrams" http://www.umlet.com/

Sequence Diagram Editors

Don’t waste your time with drawing programs when you can just write something similar to psuedocode.

Lucene Search

Browse lucene indices with Luke http://www.getopt.org/luke/

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